After all this debating and research, our room on JVD just opened up for our last night so we're staying there. Just canceled Secret Harbour.

Now, we just need to decide which ferries to take to catch our flight leaving STT at 4:53 pm:

9am Great Harbour to West End, 11:30 am Road Town to Charlotte Amalie - leaning toward this option to have shorter taxi ride to airport on STT
9am Great Harbour to West End, 11:30 am West End to Red Hook (stops in Cruz Bay to clear customs) - is this better than the option above? Is it faster to clear customs in Cruz Bay vs Charlotte Amalie?
7am Great Harbour to West End, 10am Road Town to Charlotte Amalie - safest bet but not our preference, we're not morning people, at all
9am Great Harbour to West End, 10am Road Town to Charlotte Amalie - is this even possible? Would be our favorite option if doable.